We were just there in December so here's our experience. I don't know if it's always like this or if they did things differently because of crowds over Christmas.
We hit the parks in time for their opening ceremonies most mornings. That early in the morning, I don't think the busses every went to POR which was really nice since the trip was so much faster without it. I don't think we ever waited more than 15 minutes for a bus that early.
Magic Kingdom always had it's own bus I believe, regardless of time of day. POFQ and POR have their own bus stops at MK.
Because POFQ was always dropped off first (well, except for coming back from DTD where the route is reversed and it's last, but there's the boats for DTD so it doesn't matter; it was raining so we chose the bus that day), it didn't matter that the bus was shared with POR, other than the number of people on the bus that is. All the resorts besides MK shared busses back.
When we'd go to the parks later in the day (any time after park opening), we did have to sit through going to all the stops at POR. It was no big deal since we had allowed plenty of time for this, but it certainly did make for a longer ride. Loading of
ECVs at POR stops was often very time consuming because people had to be moved from their seats in order to lift the seat for the
ECV spot. Loading ECVs is always easiest on an empty bus (which is why they don't allow anybody on until they're loaded) but this isn't possible for people getting on at POR. This didn't happen often and I felt bad for them when it did. It's certainly something I'd mention to anybody considering staying at POR with an ECV.
We loved the transportation at POFQ. It's definitely one of the many things that will keep it on my short list of resorts to consider for future trips.